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    Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds

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    Author
    Konagurthu, AS; Stuckey, PJ
    Date
    2006-04-01
    Source Title
    JOURNAL OF COMPUTATIONAL BIOLOGY
    Publisher
    MARY ANN LIEBERT, INC
    University of Melbourne Author/s
    Stuckey, Peter; KONAGURTHU, ARUN SIDDHARTHA
    Affiliation
    Computer Science and Software Engineering
    Metadata
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    Document Type
    Journal Article
    Citations
    Konagurthu, A. S. & Stuckey, P. J. (2006). Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds. JOURNAL OF COMPUTATIONAL BIOLOGY, 13 (3), pp.668-685. https://doi.org/10.1089/cmb.2006.13.668.
    Access Status
    This item is currently not available from this repository
    URI
    http://hdl.handle.net/11343/29304
    DOI
    10.1089/cmb.2006.13.668
    Abstract
    Alignment of sequences is an important routine in various areas of science, notably molecular biology. Multiple sequence alignment is a computationally hard optimization problem which involves the consideration of different possible alignments in order to find an optimal one, given a measure of goodness of alignments. Dynamic programming algorithms are generally well suited for the search of optimal alignments, but are constrained by unwieldy space requirements for large numbers of sequences. Carrillo and Lipman devised a method that helps to reduce the search space for an optimal alignment under a sum-of-pairs measure using bounds on the scores of its pairwise projections. In this paper, we generalize Carrillo and Lipman bounds and demonstrate a novel approach for finding optimal sum-of-pairs multiple alignments that allows incremental pruning of the optimal alignment search space. This approach can result in a drastic pruning of the final search space polytope (where we search for the optimal alignment) when compared to Carrillo and Lipman's approach and hence allows many runs that are not feasible with the original method.
    Keywords
    Artificial Intelligence and Image Processing

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